Status
The genome of Populus trichocarpa is estimated to be approximately 480 million base pairs contained in 19 chromosomes, and is being sequenced to approximately 7.5X depth.
The annotation v1.1 JamboreeModels includes a total of 45,555 gene models produced through the collaboration of JGI, ORNL and Ghent University (Belgium) annotation teams, and composed of known P. trichocarpa genes mapped to the genomic sequence, gene models built by homology to known plant proteins, and ab initio gene predictions. The models were consolidated and annotated using the JGI annotation pipeline. Genomic conservation with A.thaliana, Populus ESTs, alignments of EST assemblies and full-length cDNAs, and homology to curated plant proteins provide support for the predicted gene models and annotations.
Further analysis and community-wide manual curation of predicted genes continues. A snapshot of improved annotations will be published on this site and submitted to GenBank by the end of 2006.
Assembly
v1.0 (June 2004): This assembly of whole genome shotgun reads was constructed with the JGI assembler, JAZZ, using paired end sequencing reads at a coverage of 7.5X. After trimming for vector and quality, over 6 Million reads were assembled into 22,136 scaffolds totaling 473.1 Mbp. Roughly half of the genome is contained in 62 scaffolds all at least 2.1 Mb in length. 143 scaffolds were assigned to the genetic map, containing 295 Mb.
Collaborators
This project is a collaborative effort involving:
- DOE Joint Genome Institute
- Joint Genome Institute1
- DOE Oak Ridge National Laboratory
- Genome Canada
- Umea Plant Science Centre
- Ghent University
1New annotation and assembly.
Genome Reference(s)
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Science. 2006 Sep 15;313(5793):1596-604. doi: 10.1126/science.1128691
Links
- The International Poplar Consortium
- Genome British Columbia
- Stanford Human Genome Center
- Populus chloroplast analysis files (from ORNL)
- PoplarDB, a Poplar functional genomics database
- PopulusDB, an open resource for tree genomics
- Deep Green - Green Plant Phylogeny Research Coordination Group
- The French Genomics Initiative for Long-Lived Species
- Tree Genomics, Biotechnology and Breeding
- Dendrome, The Forest Tree Genome Database
- POPYOMICS